Organ-Specific Distribution and Functions of Major Secondary Metabolites in Tomato

Tomato is an economically important crop, and its secondary metabolites produced in leaves, fruits, and roots are crucial for environmental stress responses and fruit quality formation. Leaf glandular trichomes mainly synthesize defensive compounds, fruit development involves metabolic transitions, and root exudates act as key signals regulating rhizosphere microbial interactions. However, a comprehensive organ-specific understanding of this metabolic network remains fragmented. This review synthesizes the general theoretical framework of plant secondary metabolism. Using tomato as a model plant, it systematically explores the compositional features, functional differentiation, and regulatory mechanisms of secondary metabolites across leaves, fruits, and roots. We emphasize how metabolic partitioning orchestrates the trade-offs among defense, quality, and symbiosis, and highlight existing knowledge gaps, including the insufficient functional characterization of root metabolites and unclear cross-organ transport mechanisms. Future studies should focus on: (1) functions of root-specific metabolites (e.g., acylsugars); (2) molecular mechanisms of long-distance transport; (3) genetic associations of metabolic reprogramming during domestication; (4) transcriptional regulation of carotenoid cleavage; and (5) domestication selection modules coordinating defense and fruit quality. Integrating spatial metabolomics, single-cell transcriptomics, and gene editing to construct a spatiotemporal regulatory network will provide a theoretical foundation for the coordinated improvement of stress resistance and fruit quality.